Home
Database
Research
About us
P19 aptamer
Description
Dion A. Daniels and Awinder K. Sohal et al. reported aptamers with affinity for neurotensin receptor NTS-1 in their article published in 2002[1].SELEX
In their work published in 2002, Dion A. Daniels and Awinder K. Sohal et al. used SELEX to isolate RNA aptamer sequences with affinity for neurotensin receptor NTS-1 from a nucleic acid library containing about 6×1014 sequences after 7 rounds of selection process[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figure is based on the prediction results of the RNA fold website by ribodraw tool to draw[1].5'-AGGACGATGCGGACAGATACGGAACTACAGAGGTCAATTACGGTGGCCACGCCAGACGACTCGCCCGA-3'
Ligand information
SELEX ligand
Neurotensin receptor type 1 is G-protein coupled receptor for the tridecapeptide neurotensin (NTS). Signaling is effected via G proteins that activate a phosphatidylinositol-calcium second messenger system. Signaling leads to the activation of downstream MAP kinases and protects cells against apoptosis (By similarity).-----From Uniprot
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| NTR (neurotensin receptor NTS-1) | P20789 | PF00001 | 47.055 kDa | MHLNSSVPQGTPGEPDAQPFSGPQSEMEATFLALSLSNGSGNTSESDTAGPNSDLDVNTDIYSKVLVTAIYLALFVVGTVGNSVTAFTLARKKSLQSLQSTVHYHLGSLALSDLLILLLAMPVELYNFIWVHHPWAFGDAGCRGYYFLRDACTYATALNVASLSVERYLAICHPFKAKTLMSRSRTKKFISAIWLASALLAIPMLFTMGLQNRSGDGTHPGGLVCTPIVDTATVKVVIQVNTFMSFLFPMLVISILNTVIANKLTVMVHQAAEQGRVCTVGTHNGLEHSTFNMTIEPGRVQALRHGVLVLRAVVIAFVVCWLPYHVRRLMFCYISDEQWTTFLFDFYHYFYMLTNALFYVSSAINPILYNLVSANFRQVFLSTLACLCPGWRHRRKKRPTFSRKPNSMSSNHAFSTSATRETLY | 3ZEV | 366274 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| P19 aptamer | 5'-AGGACGATGCGGACAGATACGGAACTACAGAGGTCAATTACGGTGGCCACGCCAGACGACTCGCCCGA-3' | NTR | 0.37 nM |
| P108 aptamer | 5'-AGGACGATGCGGGGAAAAGATGGTATGGGCCCTAGAAAGTCCACCCGGCGCCCAGACGACTCGCCCGA-3' | NTR | 5 nM |
| P101 aptamer | 5'-AGGACGATGCGGGCGACTCCTGTACTCGAANGACAGACAGTTCCAGCCTCCAGCAGACGACTCGCCCGA-3' | NTR | 19 nM |
Similar compound
We used the Dail server website to compare the structural similarities of ligand proteins, and chose the top 10 in terms of similarity for presentation. The Dali server is a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB). Z-score is a standard score that is converted from an original score. The list of neighbours is sorted by Z-score. Similarities with a Z-score lower than 2 are spurious. RMSD (Root Mean Square Deviation) value is used to measure the degree to which atoms deviate from the alignment position.
| PDB | Z-socre | RMSD | Description |
|---|---|---|---|
| 4XES-A | 36.6 | 1.7 | Neurotensin receptor type 1, endolysin chimera |
| 6TPN-A | 32.3 | 2.3 | Orexin receptor type 2,glga glycogen synthase, Ore |
| 7XN9-A | 30.4 | 2.5 | Somatostatin receptor type 2,endo-1,4-beta-Xylana |
| 8XGR-R | 28.9 | 2.6 | Guanine nucleotide-binding protein G(I)/G(S)/G(O) |
| 6TPK-A | 27.5 | 2.2 | Oxytocin receptor |
| 7K15-A | 27.4 | 3.0 | Leukotriene b4 receptor 1, flavodoxin, leukotriene |
| 5K2A-A | 26.6 | 2.7 | Adenosine receptor A2A/soluble cytochrome B562 CH |
| 7F1T-A | 25.7 | 3.3 | C-C motif chemokine 3, C-C chemokine receptor type |
| 6LW5-A | 25.3 | 2.7 | Soluble cytochrome B562, N-formyl peptide receptor |
| 5WB2-A | 24.3 | 3.2 | Envelope protein US28, nanobody 7 fusion protein |
References
[1] Generation of RNA aptamers to the G-protein-coupled receptor for neurotensin, NTS-1.Daniels, D. A., Sohal, A. K., Rees, S., & Grisshammer, R.
Analytical biochemistry, 305(2), 214–226. (2002)